File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 32536ms, 88.42% of 36798ms total Dropped 833 nodes (cum <= 183.99ms) flat flat% sum% cum cum% 0 0% 0% 36636ms 99.56% __libc_start_call_main 0 0% 0% 36636ms 99.56% __libc_start_main_impl 0 0% 0% 36636ms 99.56% _start 0 0% 0% 36619ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 36619ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 36619ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 36619ms 99.51% main 0 0% 0% 36577ms 99.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 36577ms 99.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 36577ms 99.40% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 2ms 0.0054% 0.0054% 36568ms 99.37% AbstractCellBasedSimulation::Solve 3ms 0.0082% 0.014% 25176ms 68.42% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0027% 0.016% 19978ms 54.29% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.027% 0.043% 19797ms 53.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 188ms 0.51% 0.55% 18491ms 50.25% AbstractTwoBodyInteractionForce::AddForceContribution 1519ms 4.13% 4.68% 15561ms 42.29% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 1ms 0.0027% 4.69% 10060ms 27.34% AbstractCellBasedSimulation::UpdateCellPopulation 4335ms 11.78% 16.47% 9792ms 26.61% std::_Rb_tree::_M_lower_bound (inline) 321ms 0.87% 17.34% 8842ms 24.03% std::_Rb_tree::find (inline) 0 0% 17.34% 8842ms 24.03% std::map::find (inline) 0 0% 17.34% 8745ms 23.76% NodeBasedCellPopulation::Update 179ms 0.49% 17.82% 8603ms 23.38% NodesOnlyMesh::GetNodeOrHaloNode 481ms 1.31% 19.13% 8407ms 22.85% AbstractMesh::GetNode 297ms 0.81% 19.94% 7928ms 21.54% NodesOnlyMesh::SolveNodeMapping 7ms 0.019% 19.96% 6489ms 17.63% DistributedBoxCollection::CalculateInteriorNodePairs 241ms 0.65% 20.61% 6365ms 17.30% boost::numeric::ublas::vector_assign (inline) 210ms 0.57% 21.18% 6254ms 17.00% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5441ms 14.79% 35.97% 5441ms 14.79% std::_Rb_tree::_S_right (inline) 25ms 0.068% 36.04% 4759ms 12.93% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0054% 36.04% 4725ms 12.84% OffLatticeSimulation::ApplyBoundaries 10ms 0.027% 36.07% 4571ms 12.42% std::__sort (inline) 0 0% 36.07% 4571ms 12.42% std::sort (inline) 9ms 0.024% 36.09% 3595ms 9.77% AbstractCellPopulation::Iterator::operator++ (inline) 1225ms 3.33% 39.42% 3590ms 9.76% boost::numeric::ublas::indexing_vector_assign 334ms 0.91% 40.33% 3561ms 9.68% AbstractCellPopulation::Iterator::IsRealCell (inline) 65ms 0.18% 40.51% 3388ms 9.21% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 27ms 0.073% 40.58% 2874ms 7.81% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 251ms 0.68% 41.26% 2721ms 7.39% std::__introsort_loop 27ms 0.073% 41.34% 2547ms 6.92% PlaneBoundaryCondition::ImposeBoundaryCondition 133ms 0.36% 41.70% 2434ms 6.61% DistributedBoxCollection::AddPairsFromBox 0 0% 41.70% 2384ms 6.48% std::__unguarded_partition_pivot (inline) 32ms 0.087% 41.78% 2272ms 6.17% AbstractCellPopulation::GetLocationIndexUsingCell 16ms 0.043% 41.83% 2176ms 5.91% PlaneBoundaryCondition::VerifyBoundaryCondition 1018ms 2.77% 44.59% 2049ms 5.57% std::__unguarded_partition (inline) 212ms 0.58% 45.17% 1883ms 5.12% std::map::operator[] (partial-inline) 2ms 0.0054% 45.18% 1839ms 5.00% std::__final_insertion_sort (inline) 131ms 0.36% 45.53% 1703ms 4.63% AbstractMesh::GetVectorFromAtoB 1692ms 4.60% 50.13% 1692ms 4.60% boost::numeric::ublas::same_impl_ex 94ms 0.26% 50.39% 1652ms 4.49% std::__unguarded_insertion_sort (inline) 596ms 1.62% 52.01% 1606ms 4.36% std::__unguarded_linear_insert (inline) 1539ms 4.18% 56.19% 1539ms 4.18% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.19% 1350ms 3.67% std::_Rb_tree::lower_bound (inline) 0 0% 56.19% 1350ms 3.67% std::map::lower_bound (inline) 1ms 0.0027% 56.19% 1262ms 3.43% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 56.19% 1262ms 3.43% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 56.19% 1233ms 3.35% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 4ms 0.011% 56.20% 1208ms 3.28% AbstractCentreBasedCellPopulation::GetDampingConstant 6ms 0.016% 56.22% 1200ms 3.26% DistributedBoxCollection::CalculateBoundaryNodePairs 1127ms 3.06% 59.28% 1127ms 3.06% boost::numeric::ublas::c_vector::operator() 17ms 0.046% 59.33% 1124ms 3.05% boost::numeric::ublas::detail::expression_type_check (inline) 201ms 0.55% 59.87% 1073ms 2.92% boost::numeric::ublas::detail::equals 48ms 0.13% 60.00% 1070ms 2.91% std::_Rb_tree_const_iterator::operator++ (inline) 157ms 0.43% 60.43% 1062ms 2.89% boost::numeric::ublas::vector_binary::size (inline) 1025ms 2.79% 63.22% 1025ms 2.79% std::_Rb_tree_increment 287ms 0.78% 64.00% 979ms 2.66% NodeAttributes::AddAppliedForceContribution 413ms 1.12% 65.12% 940ms 2.55% __GI___libc_free 161ms 0.44% 65.56% 898ms 2.44% std::__new_allocator::allocate (inline) 50ms 0.14% 65.69% 887ms 2.41% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0027% 65.69% 858ms 2.33% AbstractCellBasedSimulation::DoCellBirth 387ms 1.05% 66.75% 847ms 2.30% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 66.75% 831ms 2.26% boost::numeric::ublas::norm_inf (inline) 481ms 1.31% 68.05% 831ms 2.26% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 68.05% 805ms 2.19% AbstractCellPopulation::WriteResultsToFiles 18ms 0.049% 68.10% 799ms 2.17% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 597ms 1.62% 69.72% 786ms 2.14% __dynamic_cast 0 0% 69.72% 777ms 2.11% Cell::GetMutationState 99ms 0.27% 69.99% 732ms 1.99% operator new 202ms 0.55% 70.54% 719ms 1.95% NodeAttributes::AddNeighbour 0 0% 70.54% 692ms 1.88% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 70.54% 692ms 1.88% boost::numeric::ublas::c_vector::plus_assign (inline) 189ms 0.51% 71.06% 630ms 1.71% __GI___libc_malloc 515ms 1.40% 72.46% 626ms 1.70% std::vector::push_back (inline) 135ms 0.37% 72.82% 597ms 1.62% Node::AddNeighbour 0 0% 72.82% 547ms 1.49% std::allocator_traits::allocate (inline) 2ms 0.0054% 72.83% 524ms 1.42% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 2ms 0.0054% 72.83% 522ms 1.42% NodeBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0054% 72.84% 520ms 1.41% AbstractCellPopulation::GetCellUsingLocationIndex 469ms 1.27% 74.11% 520ms 1.41% _int_free 0 0% 74.11% 512ms 1.39% std::_Rb_tree::_M_create_node (inline) 508ms 1.38% 75.49% 509ms 1.38% Node::ConstructNodeAttributes (inline) 0 0% 75.49% 453ms 1.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 442ms 1.20% 76.69% 442ms 1.20% Node::GetIndex 0 0% 76.69% 441ms 1.20% Cell::HasCellProperty (inline) 3ms 0.0082% 76.70% 441ms 1.20% CellPropertyCollection::HasProperty 3ms 0.0082% 76.71% 435ms 1.18% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 435ms 1.18% 77.89% 435ms 1.18% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.89% 431ms 1.17% boost::numeric::ublas::norm_2 (inline) 347ms 0.94% 78.84% 431ms 1.17% boost::numeric::ublas::vector_norm_2::apply (inline) 5ms 0.014% 78.85% 429ms 1.17% Cell::ReadyToDivide 0 0% 78.85% 425ms 1.15% std::_Rb_tree::_M_get_node (inline) 214ms 0.58% 79.43% 417ms 1.13% std::_Rb_tree::_M_erase 21ms 0.057% 79.49% 401ms 1.09% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.0082% 79.50% 396ms 1.08% AbstractCellProperty::IsSubType (inline) 34ms 0.092% 79.59% 385ms 1.05% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 79.59% 385ms 1.05% boost::numeric::ublas::vector::vector (inline) 27ms 0.073% 79.66% 377ms 1.02% std::_Rb_tree::_M_copy (inline) 165ms 0.45% 80.11% 370ms 1.01% Node::GetRadius 69ms 0.19% 80.30% 350ms 0.95% std::_Rb_tree::_M_clone_node (inline) 5ms 0.014% 80.31% 342ms 0.93% NodeBasedCellPopulation::UpdateMapsAfterRemesh 27ms 0.073% 80.38% 341ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 80.38% 341ms 0.93% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.38% 336ms 0.91% boost::numeric::ublas::inner_prod (inline) 0 0% 80.38% 335ms 0.91% std::_Rb_tree::_Alloc_node::operator() (inline) 89ms 0.24% 80.63% 335ms 0.91% std::__move_median_to_first (inline) 27ms 0.073% 80.70% 334ms 0.91% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 80.70% 334ms 0.91% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 158ms 0.43% 81.13% 324ms 0.88% _int_malloc 1ms 0.0027% 81.13% 321ms 0.87% NodesOnlyMesh::ReMesh 9ms 0.024% 81.16% 321ms 0.87% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0082% 81.16% 311ms 0.85% NodesOnlyMesh::UpdateNodeIndices 305ms 0.83% 81.99% 309ms 0.84% boost::detail::sp_counted_base::release 0 0% 81.99% 300ms 0.82% NodesOnlyMesh::UpdateBoxCollection 5ms 0.014% 82.01% 298ms 0.81% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 10ms 0.027% 82.03% 284ms 0.77% DistributedBoxCollection::GetProcessOwningNode 15ms 0.041% 82.08% 284ms 0.77% boost::numeric::ublas::vector_reference::operator() (inline) 274ms 0.74% 82.82% 274ms 0.74% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 82.82% 274ms 0.74% boost::numeric::ublas::c_vector::assign (inline) 270ms 0.73% 83.55% 270ms 0.73% [libchaste_cell_based.so] 96ms 0.26% 83.81% 256ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 83.81% 250ms 0.68% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.81% 248ms 0.67% VtkMeshWriter::WriteFiles 241ms 0.65% 84.47% 241ms 0.65% boost::numeric::ublas::c_vector::size (inline) 241ms 0.65% 85.12% 241ms 0.65% boost::shared_ptr::operator-> (inline) 0 0% 85.12% 236ms 0.64% boost::numeric::ublas::vector_reference::size (inline) 8ms 0.022% 85.15% 233ms 0.63% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0027% 85.15% 232ms 0.63% std::set::set (inline) 231ms 0.63% 85.78% 231ms 0.63% Node::rGetLocation 0 0% 85.78% 230ms 0.63% std::_Rb_tree::clear (inline) 226ms 0.61% 86.39% 226ms 0.61% NodeBasedCellPopulation::GetNode 3ms 0.0082% 86.40% 226ms 0.61% NodesOnlyMesh::AddNodesToBoxes 0 0% 86.40% 225ms 0.61% boost::numeric::ublas::vector_binary::operator() (inline) 103ms 0.28% 86.68% 224ms 0.61% std::__find_if (inline) 0 0% 86.68% 224ms 0.61% std::find_if (inline) 0 0% 86.68% 224ms 0.61% std::none_of (inline) 26ms 0.071% 86.75% 223ms 0.61% std::__new_allocator::deallocate (inline) 0 0% 86.75% 221ms 0.6% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.75% 221ms 0.6% vtkXMLWriterBase::Write 0 0% 86.75% 220ms 0.6% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.75% 220ms 0.6% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.75% 219ms 0.6% vtkCompositeDataPipeline::ExecuteData 0 0% 86.75% 219ms 0.6% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.75% 217ms 0.59% vtkExecutive::CallAlgorithm 0 0% 86.75% 217ms 0.59% vtkXMLUnstructuredDataWriter::ProcessRequest 3ms 0.0082% 86.76% 214ms 0.58% AbstractCellProperty::IsType (inline) 214ms 0.58% 87.34% 214ms 0.58% Node::CheckForNodeAttributes 0 0% 87.34% 207ms 0.56% NodesOnlyMesh::ResizeBoxCollection 11ms 0.03% 87.37% 206ms 0.56% NodesOnlyMesh::IsANodeCloseToDomainBoundary 206ms 0.56% 87.93% 206ms 0.56% [libchaste_mesh.so] 157ms 0.43% 88.36% 195ms 0.53% Node::AddAppliedForceContribution 0 0% 88.36% 192ms 0.52% std::_Rb_tree::_M_drop_node (inline) 0 0% 88.36% 190ms 0.52% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.36% 190ms 0.52% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 23ms 0.063% 88.42% 185ms 0.5% std::__insertion_sort (inline)